Phage Genome Editing Service

OverviewServicesSample RequirementsAdvantagesApplicationsFAQs

Overview

Phage genome editing applies targeted genetic modification to bacteriophages — the viruses that infect bacteria — to reshape host range, lytic behavior, and cargo capacity. As antimicrobial resistance rises, engineered phages are advancing from research tools toward preclinical therapeutic candidates, agricultural biocontrol agents, and programmable tools for synthetic biology.

Creative BioMart Microbe provides Phage Genome Editing Services spanning lytic, temperate, and tool-development platforms. Our workflows combine CRISPR-Cas counter-selection, recombineering (Bacteriophage Recombineering of Electroporated DNA; BRED), homologous recombination, and replicative-form (RF) reverse genetics with helper-phage display systems, backed by computational prophage prediction, giving researchers and developers a single partner from sequence to validated, scalable phage.

Whether you need anti-biofilm phage therapy against Staphylococcus aureus, broad-host-range vectors for Klebsiella pneumoniae, or a temperate λ chassis for genetic delivery, our team matches the editing strategy to your host and goal. Explore our related phage capabilities, including phage fermentation and large-scale production, to plan a complete development path.

Illustrated overview of the four phage genome editing platforms: lytic phage engineering, temperate phage engineering, phage-derived tool development, and filamentous display phage engineering, showing representative phage systems and their applications.
Figure 1. Overview of the phage genome editing platform — four integrated systems covering lytic phage engineering (T7, S. aureus, K. pneumoniae), temperate phage engineering (λ, S. aureus), phage-derived tool development (λ-Cas systems), and filamentous display phage engineering (M13), each tailored to therapeutic, delivery, or synthetic biology goals.

Our Phage Genome Editing Platforms

Four integrated platforms let us tailor each project to its intended use, from direct bacterial killing to programmable genetic delivery and display.

Platform	Focus	Representative Systems	Typical Use
Lytic Phage Engineering	Therapeutic phage development and host-range expansion	T7, S. aureus myophages, K. pneumoniae phages	Rapid bacterial killing, anti-biofilm therapy
Temperate Phage Engineering	Lysogeny control, prophage manipulation, genetic cargo delivery	λ, temperate S. aureus phages	Bacterial gene delivery, synthetic biology chassis, prophage induction studies
Phage-Derived Tool Development	Engineered phage components as programmable genome editing tools	λ-Cas12a, CRISPR-phage systems	Precision microbiome modulation, targeted antimicrobials
Filamentous / Display Phage Engineering	Non-lytic engineering for phage display, nanomaterial templating, and cargo delivery	M13	Antibody and peptide screening, nanowire scaffolding, strain-specific CRISPR delivery

Services

Service Workflow

Each project moves through a standardized six-stage pipeline — from host matching to a deliverable phage — with the editing strategy customized per phage system and target.

Horizontal six-step workflow banner for phage genome editing: isolate and match, sequence and predict, design strategy, modify and purify, validate and QC, scale up.

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Service Details

3D illustration of a Staphylococcus aureus phage with tail fibers attaching to a bacterial cell amid amber culture medium.

S. aureus Engineered Phage Development & Genome Editing

Host-specific engineering of S. aureus phages, including methicillin-resistant S. aureus (MRSA)-targeting vectors, using CRISPR/Cas9 counter-selection and homologous recombination, deploying the restriction-modification-deficient recipient RN4220 to overcome Gram-positive DNA-delivery barriers. We modify tail-fiber and receptor-binding genes to expand host range and insert anti-biofilm cargo. Each project delivers plaque-purified, sequence-verified phage with a full editing report.

3D illustration of a lambda phage with an icosahedral head and long non-contractile tail near a bacterial chromosome representing prophage integration.

λ Phage Engineering & Genome Editing

The classic temperate model for lysogeny and delivery engineering. We edit the λ genome with CRISPR-Cas9 counter-selection as the primary route, supported by BRED and in vitro assembly — controlling the lytic–lysogenic switch, inserting genetic cargo, engineering J-protein host range, and building larger-capacity λ vectors. Projects support bacterial gene delivery, synthetic biology chassis, and prophage induction studies.

3D illustration of a Klebsiella pneumoniae cell with a capsule layer and a phage displaying a depolymerase tail spike.

K. pneumoniae Engineered Phage Development & Genome Editing

Engineering of K. pneumoniae phages to cross capsular serotype barriers and target carbapenem-resistant K. pneumoniae (CRKP). We design broad-host-range derivatives by modifying tail and depolymerase genes, then validate killing across diverse clinical isolates. Deliverables include edited phage and host-range characterization.

3D illustration of a T7 phage with an icosahedral head and short tail releasing progeny particles in culture.

T7 Phage Engineering & Genome Editing

Leveraging the robust lytic cycle and T7 RNA polymerase-driven expression, we engineer T7 phage for rapid bacterial killing and diagnostics. CRISPR-Cas counter-selection and fragment assembly enable knockout, insertion, and point mutations. Each edited clone is plaque-purified and whole-genome sequenced.

3D illustration of a long filamentous M13 phage with displayed peptide loops along its coat protein surface.

M13 Phage Engineering & Genome Editing

Filamentous, non-lytic M13 engineering for phage display and targeting. We construct display libraries on pIII/pVIII and modify coat proteins for antibody engineering, nanomaterial scaffolding, and bacterial targeting. Non-lytic replication supports high-titer stable propagation. Deliverables include engineered library and screening-ready phage.

3D illustration of a computer screen displaying a bacterial genome browser with a highlighted prophage region and annotation tracks.

In Silico Prophage Discovery for Phage Engineering

A computational service that converts raw bacterial genome data into annotated, editing-ready prophage loci. We run multiple prophage prediction algorithms in parallel for consensus detection, refine attL/attR boundaries, map functional modules, and score rebooting feasibility. Outputs — annotated prophage genomes (FASTA + GFF3/GBK) and a ranked engineering target report — feed directly into our downstream phage genome editing pipeline.

Service Specifications & QC Standards

Genome Editing Strategies

Strategy	Mechanism	Best For
CRISPR-Cas counter-selection	Cas nuclease clears wild-type phage, enriching mutants	Point mutations, knockouts, insertions across lytic and temperate phages
Recombineering (BRED)	Recombination proteins mediate markerless editing in infected cells	In-frame deletions, small insertions, gene substitution
Homologous recombination	Donor plasmid exchange during infection	Large fragment replacement, cargo integration
Yeast / in vitro assembly	Fragment cloning and reboot	Whole-genome recoding, synthetic phage construction

Deliverables & QC

Plaque-purified, high-titer phage lysate.
Targeted Sanger sequencing or whole-genome sequencing confirmation of the edit, depending on complexity.
Off-target and wild-type background assessment.
Host-range and lytic-spectrum characterization where relevant.
Project report with sgRNA or primer sequences and methods.

Sample Requirements

To initiate a project, provide as much of the following as possible. Our team will advise on any gaps during the consultation.

Required Information	Optional Information	Not Accepted
Target phage (isolated lysate or deposited strain) and/or host bacterial strain Desired edit: gene knockout, point mutation, insertion, or host-range change, with target coordinates where known Intended application and downstream use (research, preclinical development, industrial)	Existing genome sequence or annotation of the phage or host Preferred editing strategy or prior attempt data Screening or bactericidal assay protocols you want mirrored	Pathogenic strains restricted by local containment law without prior approval Hosts requiring BSL-3 containment unless pre-authorized Samples lacking any host or sequence context

Note: All engineered phage constructs comply with local GMO/GMM regulations and NIH Guidelines for recombinant DNA research.

Recommended Input Format by Project Type

Project Type	Preferred Input	Estimated Timeline
Targeted point mutation / knockout	Phage lysate + host strain + target gene	3–5 weeks
Host-range expansion	Phage + multiple host isolates	4–8 weeks
Phage display library	Phage vector + insert design	4–6 weeks
Prophage prediction	Bacterial genome sequence (FASTA/FASTQ)	2–3 weeks

Timeline varies by project complexity and host system; estimated ranges assume standard conditions and prompt client feedback.

Lysates should be shipped on dry ice with glycerol backups; genomic DNA is accepted in ethanol or TE at 4°C. Contact our team via contact us before sending BSL-2 materials.

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Our Advantages

Broad host-range expertise — Editing coverage spans Gram-positive pathogens such as S. aureus and Gram-negative systems including K. pneumoniae and E. coli (λ, T7).
Integrated computation + experiment — Our in silico prophage discovery pipeline feeds directly into downstream phage genome editing, turning computational prediction into engineering-ready targets.
Scalable production with quality documentation — Edited phages transition to phage fermentation and large-scale production with batch records and documentation structured to support downstream regulatory filing.
Customizable host range and lytic spectrum — Tail-fiber, depolymerase, and regulatory-circuit engineering tune both target recognition and lytic output to your specification.
Markerless, regulatory-conscious editing — BRED-based edits can preserve a marker-free genotype, supporting streamlined regulatory submissions and publication.

Applications

3D icon of an engineered phage attaching to and lysing a bacterial cell representing phage therapy.

Phage Therapy & Personalized Antibacterial Treatments

Engineered phages deliver precision antibacterial activity against multidrug-resistant infections, including MRSA and CRKP, with host-range tuning for personalized regimens.

3D icon of a crop plant protected by phage particles representing agricultural biocontrol.

Agricultural Biocontrol & Food Safety

Phage engineering supports crop-pathogen biocontrol and food-safety decontamination, reducing reliance on chemical antimicrobials across the supply chain.

3D icon of a fermentation vessel with phage controlling contamination representing industrial bioprocessing.

Industrial Fermentation Optimization

Engineered phages serve as precision biocontrol agents to manage bacterial contamination in fermentation, while prophage curing of production strains reduces spontaneous phage induction and improves strain stability.

3D icon of a filamentous phage display scaffold linked to a genetic circuit representing synthetic biology.

Synthetic Biology & Phage Display Technologies

Temperate and filamentous phages serve as chassis and display platforms for genetic circuits, nanomaterial scaffolding, and high-throughput peptide discovery.

FAQs

Q: What is the difference between lytic and temperate phage editing approaches?

A: Lytic phages (e.g., T7) complete their cycle by host lysis and are edited for rapid killing, display, or diagnostics. Temperate phages (e.g., λ) can integrate as prophages; their editing adds lysogeny control and cargo delivery via circuits such as cI/cro regulatory circuits or CRISPR-based circuits. We select the platform by your intended use and host.

Q: What are the typical turnaround timelines for each phage system?

A: Targeted point mutations and knockouts typically require 3–5 weeks; host-range expansion across multiple isolates 4–8 weeks; phage display library construction 4–6 weeks; and computational prophage prediction 2–3 weeks. Timelines extend if novel hosts or BSL-2/3 containment is involved.

Q: How do you handle biosafety and containment for engineered phages?

A: Engineered phages are developed under BSL-1/2 containment appropriate to the host. Temperate and CRISPR-carrying constructs are sequenced and characterized to confirm no unintended virulence or mobilizable elements. BSL-3-restricted hosts require prior authorization before project initiation.

Q: Can you work with customer-provided host strains or phages?

A: Yes. We routinely edit customer-supplied phages and propagate them on your designated host strains, provided the strains are documented and permitted under local containment rules. Share genome sequences and any prior editing attempts during consultation to accelerate design.

Q: Which editing strategy do you recommend for large phage genomes?

A: For genomes that are difficult to clone, we favor BRED or λ-Red recombineering, which deliver edits directly into infected cells, and fragment-assembly reboot. CRISPR-Cas counter-selection is then applied to enrich the rare edited mutants and suppress wild-type background.

Q: Do you provide markerless edited phages?

A: Yes. Recombineering-based edits can be introduced without selectable markers, preserving a marker-free genotype where applicable. This supports regulatory submissions and downstream therapeutic translation. We document the markerless design in the project report.

Q: How do edited phages transition to larger-scale production?

A: Validated edited phages hand off to our phage fermentation and large-scale production service, which operates documentation-ready workflows suitable for research-scale and preclinical development. Preclinical studies require additional regulatory and ethical approvals.

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